Two years after clearing nine Muslim men of any involvement in the 2006 Malegaon blasts, the NIA has opposed their discharge.

There are reasons to believe this latest self-contradiction, in a case where India's premier investigation agency has been remarkably inconsistent, is bound to cause a storm.

By opposing their discharge, the agency is essentially arguing for the nine Muslims to be tried. But then it hasn't placed any new evidence on record against them.

In this very case, the former Special Public Prosecutor Rohini Salian had resigned after accusing the NIA of pressuring her to go soft on the Hindu extremists accused of actually carrying out the bombings.

Salian had also alleged that a few years before she resigned, she had sought NIA's permission to discharge the Muslim accused, only to see the officers in-charge "dilly-dally".

On 12 April, the current Special Public Prosecutor Prakash Shetty told the court hearing the case that it wasn't the "right stage" to evaluate the evidence against the two sets of accused (Hindus and Muslims) independently and "therefore it is my humble submission that they (the Muslims accused) should not be discharged".

Blood trail

In a series of blasts near a mosque in Malegaon in 2006, at least 31 people were killed and over 300 people injured. The Maharashtra ATS had arrested nine people for the bombings - all Muslim - and chargesheeted them in late 2006. The CBI, which was later handed over the investigation, filed another chargesheet against the same men in 2010.

Blasts near a Malegaon mosque in 2006 killed 31 people and injured over 300. Who was responsible?

In 2011, the NIA took over the probe. Following a confession by Swami Aseemanand that the blasts were the handiwork of Hindu extremists, the agency booked a new set of people, including a serving army officer Lt Col Srikant Purohit and Sadhvi Pragya Singh Thakur. Until recently, the NIA firmly believed that this group of people had carried out the bombings.

The NIA not only rubbished the findings of the ATS and the CBI, it stated on record that the witnesses brought by the ATS against the Muslim accused had been "pressurised".

The nine Muslim accused then filed an application for discharge, only to see the NIA go back on its stand in court Tuesday.

Lawyer Sarim Naved: Was all NIA's evidence against Aseemanand and his accomplices cooked up then?

Fair probe?

The latest change-of-heart means that the NIA would now be arguing for the trial of two different sets of accused in the same case. This doesn't just sound illogical, it might not even be legal.

"You can't tell a court that you believe two different sets of people committed the same crime," argued Sarim Naved, who is representing one of the victims in the case.

Naved said if the NIA wanted the other set of accused - the Muslims - to stand trial, the agency would not only have to produce new evidence, but trash its earlier line of investigation as well.

"NIA will have to explain why their officers were probing an incorrect line all along - it couldn't simply have been a case of inefficiency. They placed statements before the court that were recorded before magistrates. So was all the evidence that was produced to support their theory that Aseemanand and his accomplices were behind this crime cooked up? Did the magistrates lie as well?" Naved asked.

This is not the first time the NIA has contradicted itself in the Malegaon case. In February, the agency told the court it intended to withdraw charges under the Maharashtra Control of Organised Crime Act against 11 of the accused, including Lt Col Purohit and Sadhvi Pragya, five years after booking them them under those very sections.

The NIA is now seeking the opinion of the Attorney General on the matter, an unusual move that's believed to be a tactic to delay filing of the chargesheet.

This coupled with NIA's discrepant views on the fundamental aspect of the case - who it believes was actually responsible for the killing of 31 people in Malegaon - casts serious doubts about the agency's independence.

He hasn't been to journalism school, as evident by his refusal to end articles with 'ENDS' or 'EOM'. Principal correspondent at Catch, Suhas studied engineering and wrote code for a living before moving to writing mystery-shrouded-pall-of-gloom crime stories. On being accepted as an intern at Livemint in 2010, he etched PRESS onto his scooter. Some more bylines followed in Hindustan Times, Times of India and Mail Today.